I would check into the repository to find a 5.3 with a similar tune, similar flowing injectors, with boost. It might be a better starting point. You can always change it back.

I did this as a basis for my 383 and it ran pretty good from the start. I just had to fine tune a few things.

 

^^^^ This. Your truck is a 2000 that came with a regulator on the rail. That supercharger was built for a system with an in tank regulator. You would have to be using a regulator on the rail for it to be working properly. You should not even be looking at tuning until you make sure you can maintain proper fuel pressure under all power levels.

Explain your whole fuel system please.

 

His IFR table is not even right in tune. This is #1 priority when changing tune for larger injectors, not to mention all the other tables. Hell his injectors may be misfiring due to the wrong values.